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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">oncotomsk</journal-id><journal-title-group><journal-title xml:lang="ru">Сибирский онкологический журнал</journal-title><trans-title-group xml:lang="en"><trans-title>Siberian journal of oncology</trans-title></trans-title-group></journal-title-group><issn pub-type="ppub">1814-4861</issn><issn pub-type="epub">2312-3168</issn><publisher><publisher-name>Tomsk National Research Medical Сепtеr of the Russian Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.21294/1814-4861-2024-23-5-35-46</article-id><article-id custom-type="elpub" pub-id-type="custom">oncotomsk-3264</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>ЛАБОРАТОРНЫЕ И ЭКСПЕРИМЕНТАЛЬНЫЕ ИССЛЕДОВАНИЯ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>LABORATORY AND EXPERIMENTAL STUDIES</subject></subj-group></article-categories><title-group><article-title>Применение экзомного секвенирования для поиска мутаций, ассоциированных с наследственными формами рака молочной железы, в этнических группах Сибири</article-title><trans-title-group xml:lang="en"><trans-title>Whole exome sequencing: the search for mutations associated with hereditary breast cancer in ethnic groups of Siberia</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-0051-8814</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Гервас</surname><given-names>П. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Gervas</surname><given-names>P. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Гервас Полина Анатольевна, кандидат медицинских наук, научный сотрудник лаборатории молекулярной онкологии и иммунологии, </p><p>634009, г. Томск, пер. Кооперативный, 5</p></bio><bio xml:lang="en"><p>Polina A. Gervas, MD, PhD, Researcher, Laboratory of Molecular Oncology and Immunology,</p><p>5, Kooperativny St., Tomsk, 634009</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-1475-1185</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Молоков</surname><given-names>А. Ю.</given-names></name><name name-style="western" xml:lang="en"><surname>Molokov</surname><given-names>A. Yu.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Молоков Алексей Юрьевич, младший научный сотрудник лаборатории молекулярной онкологии и иммунологии, </p><p>634009, г. Томск, пер. Кооперативный, 5</p></bio><bio xml:lang="en"><p>Aleksey Yu. Molokov, Junior Researcher, Laboratory of Molecular Oncology and Immunology, </p><p>5, Kooperativny St., Tomsk, 634009</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-0562-3878</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Бабышкина</surname><given-names>Н. Н.</given-names></name><name name-style="western" xml:lang="en"><surname>Babyshkina</surname><given-names>N. N.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Бабышкина Наталия Николаевна, доктор медицинских наук, старший научный сотрудник лаборатории молекулярной онкологии и иммунологии,</p><p>634009, г. Томск, пер. Кооперативный, 5</p></bio><bio xml:lang="en"><p>Nataliya N. Babyshkina, MD, DSc, Senior Researcher, Laboratory of Molecular Oncology and Immunology, </p><p>5, Kooperativny St., Tomsk, 634009</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Иванова</surname><given-names>Ф. Г.</given-names></name><name name-style="western" xml:lang="en"><surname>Ivanova</surname><given-names>F. G.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Иванова Феодосия Гавриловна, кандидат медицинских наук, заведующая отделением противоопухолевой лекарственной терапии, </p><p>677000, г. Якутск, ул. Петра Алексеева, 89</p></bio><bio xml:lang="en"><p>Feodosia G. Ivanova, MD, PhD, Head of Department of Drug Treatment,</p><p>89, Petra Alekseeva St., Yakutsk, 677000</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Николаева</surname><given-names>Т. И.</given-names></name><name name-style="western" xml:lang="en"><surname>Nikolaeva</surname><given-names>T. I.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Николаева Татьяна Ивановна, кандидат медицинских наук, главный врач, </p><p>677000, г. Якутск, ул. Петра Алексеева, 89</p></bio><bio xml:lang="en"><p>Tatiana I. Nikolaeva, MD, PhD, Chief Physician, </p><p>89, Petra Alekseeva St., Yakutsk, 677000</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-3385-9471</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Тихонов</surname><given-names>Д. Г.</given-names></name><name name-style="western" xml:lang="en"><surname>Tikhonov</surname><given-names>D. G.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Тихонов Дмитрий Гаврильевич, доктор медицинских наук, профессор, главный научный сотрудник, </p><p>677000, г. Якутск, ул. Белинского, 58</p></bio><bio xml:lang="en"><p>Dmitrii G. Tikhonov, MD, DSc, Professor, Chief Researcher, </p><p>58, Belinsky St., Yakutsk, 677000</p></bio><xref ref-type="aff" rid="aff-3"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-3651-0665</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Чойнзонов</surname><given-names>Е. Л.</given-names></name><name name-style="western" xml:lang="en"><surname>Choynzonov</surname><given-names>E. L.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Чойнзонов Евгений Лхамацыренович, доктор медицинских наук, профессор, академик РАН, директор, </p><p>634009, г. Томск, пер. Кооперативный, 5</p></bio><bio xml:lang="en"><p>Evgeny L. Choynzonov, MD, DSc, Professor, Full Member of the Russian Academy of Sciences, Director,</p><p>5, Kooperativny St., Tomsk, 634009</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-1526-9013</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Чердынцева</surname><given-names>Н. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Cherdyntseva</surname><given-names>N. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Чердынцева Надежда Викторовна, доктор биологических наук, профессор, член-корреспондент РАН, заместитель директора по научной работе, заведующая лабораторией молекулярной онкологии и иммунологии, </p><p>634009, г. Томск, пер. Кооперативный, 5</p></bio><bio xml:lang="en"><p>Nadezhda V. Cherdyntseva, DSc, Professor, Corresponding Member of the Russian Academy of Sciences, Deputy Director for Science, Head of the Department of Molecular Oncology and Immunology, </p><p>5, Kooperativny St., Tomsk, 634009</p></bio><xref ref-type="aff" rid="aff-1"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru"><institution>Научно-исследовательский институт онкологии, Томский национальный исследовательский медицинский центр Российской академии наук</institution><country>Россия</country></aff><aff xml:lang="en"><institution>Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences</institution><country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru"><institution>ГБУ РС(Я) «Якутский республиканский онкологический диспансер»</institution><country>Россия</country></aff><aff xml:lang="en"><institution>Yakut Republican Cancer Center</institution><country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-3"><aff xml:lang="ru"><institution>Медицинский институт, Северо-Восточный федеральный университет им. М.К. Аммосова</institution><country>Россия</country></aff><aff xml:lang="en"><institution>Medical Institute, M.K. Ammosov North-Eastern Federal University</institution><country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2024</year></pub-date><pub-date pub-type="epub"><day>06</day><month>11</month><year>2024</year></pub-date><volume>23</volume><issue>5</issue><fpage>35</fpage><lpage>46</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Гервас П.А., Молоков А.Ю., Бабышкина Н.Н., Иванова Ф.Г., Николаева Т.И., Тихонов Д.Г., Чойнзонов Е.Л., Чердынцева Н.В., 2024</copyright-statement><copyright-year>2024</copyright-year><copyright-holder xml:lang="ru">Гервас П.А., Молоков А.Ю., Бабышкина Н.Н., Иванова Ф.Г., Николаева Т.И., Тихонов Д.Г., Чойнзонов Е.Л., Чердынцева Н.В.</copyright-holder><copyright-holder xml:lang="en">Gervas P.A., Molokov A.Y., Babyshkina N.N., Ivanova F.G., Nikolaeva T.I., Tikhonov D.G., Choynzonov E.L., Cherdyntseva N.V.</copyright-holder><license xml:lang="ru" license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>Данная работа распространяется под лицензией Creative Commons Attribution 4.0.</license-p></license><license xml:lang="en" license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://www.siboncoj.ru/jour/article/view/3264">https://www.siboncoj.ru/jour/article/view/3264</self-uri><abstract><p>Наследственный рак молочной железы (нРМЖ) представляет собой гетерогенное онкологическое заболевание, обусловленное мутациями ряда генов, характеризующихся этноспецифичностью. Клиническая гетерогенность данного заболевания существенно осложняет его диагностику. Применение метода высокопроизводительного секвенирования является одним из возможных подходов, позволяющих проводить поиск генов и их вариантов, приводящих к формированию нРМЖ.</p><p>Целью исследования явился поиск новых генов и их вариантов, связанных с нРМЖ в этнических группах Сибири, с использованием метода секвенирования экзома.</p><sec><title>Материал и методы</title><p>Материал и методы. В исследование включено 16 пациенток с РМЖ (тувинки, якутки, алтайки). Материалом исследования служила геномная ДНК, выделенная из лейкоцитов периферической крови. Библиотеки были подготовлены с использованием набора BGI Optimal DNA Library Prep. Для гибридизации использовался набор Agilent SureSelect Human All Exon V6. Высокопроизводительное секвенирование было выполнено на платформе DNBSeq-G400. Данные секвенирования экзома были обработаны с использованием DRAGEN Bio-IT v.3.9.5 (Illumina) и выровнены на референсный человеческий геном hg38. Качество данных секвенирования контролировалось с помощью программного обеспечения MultiQC v.1.11.</p></sec><sec><title>Результаты</title><p>Результаты. В общей группе пациенток с признаками нРМЖ патогенные варианты были обнаружены в 12,5 % (2/16). Патогенный вариант гена BRCA1 (c.3087_3088del: p.R1029fs, rs80357635) был выявлен у молодой пациентки с метахронным РМЖ (этническая группа якуты). Патогенный вариант гена ATM (rs780619951 NM_000051:exon16:c.C2413T:p.R805X) был выявлен у молодой пациентки с РМЖ (этническая группа тувинцы). Патогенный вариант гена репарации ДНК TDP2 c.G4T: p.E2X, rs770844602 был впервые выявлен у тувинки с метахронным РМЖ и с семейным анамнезом. Вклад гена репарации ДНК TDP2 в патогенез РМЖ еще предстоит изучить. Вариант гена TDG (rs764159587 NM_001363612:exon7:c.536dupA:p. E179fs), обнаруженный в тувинском этносе и влияющий на сплайсинг (SpliceAI: 0.580), требует особого внимания.</p></sec><sec><title>Заключение</title><p>Заключение. Впервые описан герминальный вариант в гене BRCA1 (c.3087_3088del: p.R1029fs, rs80357635), связанный с РМЖ, в этнической группе якутов. Необходимы дальнейшие исследования для изучения роли герминальных вариантов генов TDP2, TDG при РМЖ.</p></sec></abstract><trans-abstract xml:lang="en"><p>Hereditary breast cancer (HBC) is a heterogeneous disease caused by mutations in genes characterized by ethnic specifcity. The clinical heterogeneity of this disease signifcantly complicates its diagnosis. The use of high-throughput sequencing is one of the approaches that allow the search for genes and their variants associated with the development of HBC. The purpose of the study was to search for new genes associated with HBC in the understudied ethnic groups of Siberia by using whole exome sequencing (WES).</p><sec><title>Material and Methods</title><p>Material and Methods. WES was performed on a cohort of 16 probands with BC (Tuvan, Yakut, Altai ethnos). The study material was genomic DNA isolated from peripheral blood leukocytes. Libraries were prepared using a BGI Optimal DNA Library Prep kit. An Agilent SureSelect Human All Exon V6 kit was used for hybridization. High-throughput sequencing was performed on a DNA nanoball sequencing platform (DNBSeq-G400).</p></sec><sec><title>Results</title><p>Results. In the overall group of patients with signs of HBC, pathogenic variants were detected in 12.5 % of cases (2/16). For the frst time, BRCA1 (rs80357635) pathogenic variant was identified in a young patient with metachronous BC (Yakut ethnic group). A pathogenic variant of the ATM gene (rs780619951 NM_000051:exon16:c.C2413T:p.R805X) was identified in a young patient with BC (Tuvinian ethnic group). A pathogenic variant of the TDP2 c.G4T:p.E2X, rs770844602 gene (DNA repair gene) was identified for the frst time in a Tuvan BC patient (metachronous) with a family history, but its contribution to HBC remains to be proven. The TDG gene variant (rs764159587 NM_001363612:exon7:c.536dupA:p.E179fs) found in the Tuvan ethnic group and affecting splicing (SpliceAI: 0.580) requires special attention.</p></sec><sec><title>Conclusion</title><p>Conclusion. This report is the frst to describe the germinal variant in the BRCA1 (rs80357635) gene in the Yakut ethnic group. Further studies are required to confrm pathogenicity of germinal variants in non-well studied genes TDP2, TDG in ethnic BC patients.</p></sec></trans-abstract><kwd-group xml:lang="ru"><kwd>полноэкзомное секвенирование</kwd><kwd>наследственные мутации</kwd><kwd>этнические группы</kwd><kwd>рак молочной железы</kwd><kwd>якутки</kwd><kwd>тувинки</kwd></kwd-group><kwd-group xml:lang="en"><kwd>exome sequencing</kwd><kwd>germline mutations</kwd><kwd>breast cancer</kwd><kwd>ethnic groups</kwd><kwd>Yakuts</kwd><kwd>Tuvans</kwd></kwd-group><funding-group><funding-statement xml:lang="ru">Исследование выполнено при финансовой поддержке РНФ, проект №23-25-00386.</funding-statement><funding-statement xml:lang="en">The reported study was funded by Russian Foundation Science according to research project No23-25-00386</funding-statement></funding-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Grann V.R., Panageas K.S., Whang W., Antman K.H., Neugut A.I. 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